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Special Issue "Gut Microbiome of Farm Animals in Health and Disease 2.0"

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A special issue of Microorganisms (ISSN 2076-2607). This special issue belongs to the section "Veterinary Microbiology".

Deadline for manuscript submissions: 15 December 2023 | Viewed by 7880

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Dr. Łukasz M. Grześkowiak

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Institute of Animal Nutrition, Freie Universität Berlin, 14195 Berlin, Germany
Interests: microbial ecology; microbiota-host cross-talk; health
Special Issues, Collections and Topics in MDPI journals

Dr. Elsa Leclerc Duarte
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Guest Editor

Department of Biology, School of Sciences and Technology and MED-Mediterranean Institute for Agriculture, Environment and Development, University of Évora, Évora, Portugal
Interests: medical microbiology; infectious diseases
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

The role of the gut microbiome in maintaining health in farm animals has been gaining increasing interest. Specifically, gut microbe-host crosstalk has been associated with animal physiology, metabolism and immunity. Early-life microbial succession in newborn offspring is essential for gut maturation and immune development and may play a significant role in animal resilience to pathogens later in life. In addition, some evidence suggests that the maternal microenvironment could play a significant role in early microbial and immune development in young animals. In intensive production systems, animals face significant stress and become more vulnerable to gut dysbiosis and illnesses. Nutrition is a strong modulating factor gut microbial ecosystems in animals. Supplying animals with certain dietary components shows promise for modulating the microbiota and their impact on the host by controlling pathogen colonisation and dissemination, and reducing the risk of diseases. Finally, uncovering the mechanisms by which the microbiome and host interact with each other is crucial for the understanding of homeostasis, to prevent or treat gut dysbiosis and illnesses.

This Special Issue aims to publish recent findings on various aspects of the gut microbiota and its ecological interactions with the animal host through cellular, metabolic, genetic and environmental pathways. Research articles, review articles and short communications on the gut microbiome in farm animals are welcome. We look forward to publishing your work.

Dr. Łukasz M. Grześkowiak
Dr. Elsa Leclerc Duarte
Guest Editors

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Microorganisms is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2200 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

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Open AccessArticle

Microbiome of Ceca from Broiler Chicken Vaccinated or Not against Coccidiosis and Fed Berry Pomaces

and

Microorganisms 2023, 11(5), 1184; https://doi.org/10.3390/microorganisms11051184 - 30 Apr 2023

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Abstract

American cranberry (Vaccinium macrocarpon) and lowbush/wild blueberry (V. angustifolium) pomace are polyphenol-rich products having potentially beneficial effects in broiler chickens. This study investigated the cecal microbiome of broiler-vaccinated or non-vaccinated birds against coccidiosis. Birds in each of the two groups (vaccinated or non-vaccinated) were fed a basal non-supplemented diet (NC), a basal diet supplemented with bacitracin (BAC), American cranberry (CP), and lowbush blueberry (BP) pomace alone or in combination (CP + BP). At 21 days of age, cecal DNA samples were extracted and analyzed using both whole-metagenome shotgun sequencing and targeted-resistome sequencing approaches. Ceca from vaccinated birds showed a lower abundance of Lactobacillus and a higher abundance of Escherichia coli than non-vaccinated birds (p < 0.05). The highest and lowest abundance of L. crispatus and E. coli, respectively, were observed in birds fed CP, BP, and CP + BP compared to those from NC or BAC treatments (p < 0.05). Coccidiosis vaccination affected the abundance of virulence genes (VGs) related to adherence, flagella, iron utilization, and secretion system. Toxin-related genes were observed in vaccinated birds (p < 0.05) in general, with less prevalence in birds fed CP, BP, and CP + BP than NC and BAC (p < 0.05). More than 75 antimicrobial resistance genes (ARGs) detected by the shotgun metagenomics sequencing were impacted by vaccination. Ceca from birds fed CP, BP, and CP + BP showed the lowest (p < 0.05) abundances of ARGs related to multi-drug efflux pumps, modifying/hydrolyzing enzyme and target-mediated mutation, when compared to ceca from birds fed BAC. Targeted metagenomics showed that resistome from BP treatment was distant to other groups for antimicrobials, such as aminoglycosides (p < 0.05). Significant differences in the richness were observed between the vaccinated and non-vaccinated groups for aminoglycosides, β-lactams, lincosamides, and trimethoprim resistance genes (p < 0.05). Overall, this study demonstrated that dietary berry pomaces and coccidiosis vaccination significantly impacted cecal microbiota, virulome, resistome, and metabolic pathways in broiler chickens. Full article

(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease 2.0)

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Open AccessArticle

Exploring the Bacterial Community in Aged Fecal Sources from Dairy Cows: Impacts on Fecal Source Tracking

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Microorganisms 2023, 11(5), 1161; https://doi.org/10.3390/microorganisms11051161 - 28 Apr 2023

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Abstract

(1) Background: This paper discusses the impact of agricultural activities on stream health, particularly in relation to dairy cow fecal pollution. The study explores the fecal microbiome of cattle and the potential ecological implications of aging fecal pollution on waterways. (2) Methods: The study examines changes in the bacterial community available for mobilization from in-situ decomposing cowpats and the effects of simulated rainfall. The microbiome of individual cowpats was monitored over 5.5 months. We used 16S rRNA metagenomics and machine learning software, FEAST (Fast Expectation-mAximization for microbial Source Tracking), for bacterial and fecal source assignments. (3) Results: The phyla Bacillota and Bacteroidota are dominant in the fecal microbiota of fresh cow feces but shift to Pseudomonodota, Actinomycetota, and environmental Bacteroidota in aged cowpats. Potential impacts of these bacterial community shifts on inputs to local agricultural streams are discussed in relation to water quality monitoring and aging sources of fecal contamination. We identified taxon orders that are potential indicators of fresh cattle sources (Oscillospirales and Bacteroidales) and aged sources (Peptostreptococcales-Tissierellales) in water bodies. (4) The paper highlights that bacterial metagenomic profiling can inform our understanding of the ecology of microbial communities in aquatic environments and the potential impacts of agricultural activities on ecosystem health. Full article

(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease 2.0)

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Open AccessArticle

The Gut Microbiota of Broilers Reared with and without Antibiotic Treatment

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Microorganisms 2023, 11(4), 876; https://doi.org/10.3390/microorganisms11040876 - 29 Mar 2023

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Abstract

The aim of this study was to examine the microbiota in broilers reared with and without antibiotics and to investigate differences between the upper, middle and lower sections of the gastrointestinal tract (GIT). One of two commercial flocks was treated with an antibiotic (T) (20 mg trimethoprim and 100 mg sulfamethoxazole per ml in the drinking water for 3 days) and the other was left untreated (UT). The GIT contents of 51 treated and untreated birds were aseptically removed from the upper (U), middle (M) and lower (L) sections. These were pooled in triplicate (n = 17 per section per flock), the DNA extracted and purified, 16S amplicon metagenomic sequencing performed and the resultant data analysed using a range of bioinformatics software. There were significant differences in the microbiota of the upper, middle and lower GIT, and treatment with the antibiotic significantly affected the microbiota in each of these sections. This study provides new data on broiler GIT microbiota and suggests that GIT location is a more important determinant of the constituent bacterial flora rather than the use or otherwise of antimicrobial treatments, at least when applied early in the production cycle. Full article

(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease 2.0)

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Open AccessArticle

Evaluation of Effectiveness of a Novel Multicomponent Mycotoxins Detoxification Agent in the Presence of AFB1 and T-2 Toxin on Broiler Chicks

Jelena Nedeljković Trailović

and

Branko Petrujkić

Microorganisms 2023, 11(3), 574; https://doi.org/10.3390/microorganisms11030574 - 24 Feb 2023

Viewed by 563

Abstract

This experimental study was conducted to determine the ability of a novel mycotoxins detoxification agent (MR) at a concentration of 0.2% to reduce the toxicity of aflatoxin B1 (AFB1) or T-2 toxin, alone or in combination, and to examine its effect on performance, pathohistological changes (PH) and the residue of these toxins in the tissues of broiler chicks. A total of 96 broiler chicks were divided into eight equal groups: group C, which served as control (without any additives); group MR, which received the novel detoxification agent (supplemented with 0.2%); group E-I (0.1 mg AFB1/kg of diet); group E-II (0.1 mg AFB1/kg of diet + MR 0.2%); group E-III (0.5 mg T-2 toxin/kg of diet); group E-IV (0.5 mg T-2 toxin/kg of diet + 0.2% MR); group E-V (combination of 0.1 mg AFB1/kg, 0.5 mg T-2 toxin/kg of diet); and group E-VI (combination of 0.1 mg AFB1/kg, 0.5 mg T-2 toxin + 0.2% MR). Results indicate that feeds containing AFB1 and T-2 toxin, alone or in combination, adversely affected the health and performance of poultry. However, the addition of MR to diets containing AFB1 and T-2 toxin singly and in combination exerted a positive effect on body weight, feed intake, weight gain, feed efficiency and microscopic lesions in visceral organs. Residual concentration of AFB1 in liver samples was significantly (p < 0.05) decreased when chicks were fed diets supplemented with 0.2% of MR. Full article

(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease 2.0)

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Open AccessArticle

Dietary Supplementation with Botanical Blends Modified Intestinal Microbiota and Metabolomics of Weaned Pigs Experimentally Infected with Enterotoxigenic Escherichia coli

Ravichandran Sripathy

and

Yanhong Liu

Microorganisms 2023, 11(2), 320; https://doi.org/10.3390/microorganisms11020320 - 27 Jan 2023

Viewed by 710

Abstract

The objective of this study was to investigate supplementation of botanical blends (BB) comprised of 0.3% capsicum oleoresin and 12% garlic oil on gut microbiota and metabolomic profiles in serum and ileal mucosa of Escherichia coli infected pigs. Sixty weaned pigs were assigned to one of five treatments: negative control (CON−), positive control (CON+), dietary supplementation of 100 ppm BB1, 50 or 100 ppm BB2. All pigs, except CON−, were orally inoculated with 10¹⁰ CFU F18 ETEC/3-mL dose for 3 consecutive days after 7 d adaption. Feces, ileal digesta and cecal content were collected for 16S rRNA amplicon sequencing. Serum and ileal mucosa underwent primary metabolomics analysis. Supplementing 100 ppm BB1 increased (p < 0.05) relative abundances of Enterobacteriaceae and Escherichia–Shigella in ileum, and the relative abundances of Bacteroidota and Prevotellaceae in cecum than CON+ on d 5 post-inoculation (PI). Supplementing 100 ppm BB2 upregulated serum pinitol on d 4 PI and serum cholesterol and aminomalonic acids on d 21 PI, while supplementing 50 ppm BB2 reduced asparagine in ileal mucosa on d 5 PI than CON+. Supplementation with botanical blends modulated ileal and cecal microbiota and serum metabolomics profiles in weaned pigs under Escherichia coli challenge. Full article

(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease 2.0)

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Open AccessArticle

Effects of Dietary Isoleucine Supplementation on the Production Performance, Health Status and Cecal Microbiota of Arbor Acre Broiler Chickens

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Microorganisms 2023, 11(2), 236; https://doi.org/10.3390/microorganisms11020236 - 17 Jan 2023

Cited by 1 | Viewed by 1353

Abstract

A total of 24,000 healthy 1-day-old Arbor Acres broilers with similar initial weights were used in this study and fed a basal diet supplemented with 0, 400 and 800 mg/kg isoleucine (Ile), denoted CON, ILE400 and ILE800, respectively. Results revealed that the final body weight, average daily weight gain, and eviscerated carcass rate, of broiler chickens in the ILE400 group were significantly higher than in other groups (p < 0.05). In addition, the ILE400 and ILE800 groups had a lower feed conversion rate and a higher survival rate and breast muscle rate (p < 0.05), while the abdominal fat rate was significantly lower than the CON group (p < 0.05). There were significantly lower serum concentrations of UREA, glucose (GLU) and total cholesterol (TCHO) in the ILE400 and ILE800 groups than in the CON group (p < 0.05); glutathione peroxidase (GSH-Px) activity was significantly higher in the ILE400 group than in the other groups, and tumor necrosis factor-alpha (TNF-α) concentration was considerably lower than in other groups (p < 0.05). Moreover, interleukin (IL)-10 concentration in the ILE800 group was significantly higher than in the other groups (p < 0.05). The ILE400 group significantly down-regulated the mRNA expressions of fatty-acid synthase (FASN) and solid alcohol regulatory element binding protein 1c (SREBP1c), and significantly up-regulated the mRNA expressions of adipose triglyceride lipase (ATGL), hormone-sensitive lipase (HSL), lipoprotein lipase (LPL) and sirtuin1 (Sirt1) (p < 0.05). The ILE400 group had significantly higher intestinal villus height than the CON and ILE800 groups, while the ILE800 group had significantly lower intestinal villus height/crypt depth (p < 0.05). Furthermore, high-throughput sequencing showed that the Shannon index, and Verrucomicrobiota, Colidextribacter and Bacteroides abundances were significantly higher in the ILE400 group than in the CON group (p < 0.05). Interestingly, the ILE800 group reduced the Simpson index, phylum Firmicutes and Bacteroidota abundances (including genera Colidextribacter, Butyricicoccus, [Ruminococcus]_torques_group, Bacteroides, Alistipes, Barnesiella and Butyricimonas), and increased Proteobacteria and Cyanobacteria (including genera Dyella, Devosia, unidentified_Chloroplast and Hyphomicrobium) (p < 0.05). Overall, our study showed that adding 400 mg/kg Ile to the diet (diets total Ile levels at 1.01%, 0.90% and 0.87% during the starter, grower and finisher phases, respectively) increased production performance and improved the health status in broiler chickens. Full article

(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease 2.0)

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Open AccessArticle

Bacterial Profiles of Brain in Downer Cattle with Unknown Etiology

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Microorganisms 2023, 11(1), 98; https://doi.org/10.3390/microorganisms11010098 - 30 Dec 2022

Viewed by 1006

Abstract

Downer cow can be caused by muscular paralysis, neurological damage, metabolic disorder, and/or the complication of microbial infection. However, downer cow with unknown etiology is issued because of the non-detection of its bacterial etiological agent. In this study, differences in the bacterial community in brain tissues between downer cattle with unknown etiology and healthy slaughtered cattle are investigated. Bacterial diversity and representative genera between downer and normal cattle were significantly different (p < 0.05). There are significant differences in representative genera of downer and normal cattle, especially the significance, fold change, and area under the receiver operating characteristic curve score (p < 0.05). Furthermore, the prediction of functional genes in brain microbiota between the downer and normal cattle revealed differences in the cluster of orthologous gene categories, such as lipid transport and metabolism, secondary metabolite biosynthesis, and signal transduction (p < 0.05). This study revealed a significant difference in microbiota between the downer and normal cattle. Thus, we demonstrate that representative genera from downer cattle through 16S rRNA gene amplicon sequencing and microbiota analysis have the potential as candidates for bacterial etiological agents for downer cow. Full article

(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease 2.0)

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Open AccessArticle

Effects of Oral Glutamine Supplementation, Birthweight and Age on Colonic Morphology and Microbiome Development in Male Suckling Piglets

Johannes Schulze Holthausen

and

Microorganisms 2022, 10(10), 1899; https://doi.org/10.3390/microorganisms10101899 - 25 Sep 2022

Viewed by 998

Abstract

Mortality, impaired development and metabolic dysfunctions of suckling low-birthweight piglets may be influenced by modulating the intestinal microbiome through glutamine supplementation. Therefore, this study examined whether glutamine supplementation may affect the colonic development and microbiome composition of male low- and normal-birthweight piglets at 5 and 12 days of age. Suckling piglets were supplemented orally with glutamine or alanine. Colonic digesta samples were obtained for 16S rDNA sequencing, determination of bacterial metabolites and histomorphological tissue analyses. Glutamine-supplemented piglets had lower concentrations of cadaverine and spermidine in the colonic digesta (p < 0.05) and a higher number of CD3⁺ colonic intraepithelial lymphocytes compared to alanine-supplemented piglets (p < 0.05). Low-birthweight piglets were characterised by a lower relative abundance of Firmicutes, the genera Negativibacillus and Faecalibacterium and a higher abundance of Alistipes (p < 0.05). Concentrations of cadaverine and total biogenic amines (p < 0.05) and CD3⁺ intraepithelial lymphocytes (p < 0.05) were lower in low- compared with normal-birthweight piglets. In comparison to the factor age, glutamine supplementation and birthweight were associated with minor changes in microbial and histological characteristics of the colon, indicating that ontogenetic factors play a more important role in intestinal development. Full article

(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease 2.0)

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Review

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Open AccessReview

The Prevalence of Aliarcobacter Species in the Fecal Microbiota of Farm Animals and Potential Effective Agents for Their Treatment: A Review of the Past Decade

Cansu Çelik

Orhan Pınar

and

Nisa Sipahi

Microorganisms 2022, 10(12), 2430; https://doi.org/10.3390/microorganisms10122430 - 08 Dec 2022

Cited by 2 | Viewed by 770

Abstract

There is an endless demand for livestock-originated food, so it is necessary to elucidate the hazard points for livestock breeding. Pathogens are one of the hazard points that threaten the biosecurity of farm-animal breeding and public health. As a potential foodborne pathogen, Aliarcobacter is a member of the intestinal microbiota of farm animals with and without diarrhea. Aliarcobacter spp. are capable of colonizing livestock intestines and are transmitted through the feces. Hence, they endanger slaughterhouses and milk products with fecal contamination. They also have other, rarer, vertical and horizontal transmission routes, including the offspring that abort in farm animals. Gastrointestinal symptoms and abort cases demonstrate potential financial losses to the industry. Viewed from this perspective, the global circulation of farm-animal products is a significant route for zoonotic agents, including Aliarcobacter. In the last decade, worldwide prevalence of Aliarcobacter in fecal samples has ranged from 0.8% in Italy to 100% in Turkey. Furthermore, antibiotic resistance is recognized as a new type of environmental pollutant and has become a hot topic in animal breeding and the food industry. Increasing antibiotic resistance has become a significant problem impacting productivity. The increase in antimicrobial resistance rates in Aliarcobacter is caused by the misuse of antimicrobial drugs in livestock animals, leading to the acquiring of resistance genes from other bacteria, as well as mutations in current resistance genes. The most resistant strains are A. butzleri, A. cryaerophilus, and A. skirrowii. This review analyzes recent findings from the past decade on the prevalence of Aliarcobacter in the intestinal microbiota and the current effective antibiotics against Aliarcobacter. The paper also highlights that A. cryaerophilus and A. skirrowii are found frequently in diarrheal feces, indicating that Aliarcobacter should be studied further in livestock diarrheal diseases. Moreover, Aliarcobacter-infected farm animals can be treated with only a limited number of antibiotics, such as enrofloxacin, doxycycline, oxytetracycline, and gentamicin. Full article

(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease 2.0)

Other

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Open AccessSystematic Review

Effects of Major Families of Modulators on Performances and Gastrointestinal Microbiota of Poultry, Pigs and Ruminants: A Systematic Approach

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Microorganisms 2023, 11(6), 1464; https://doi.org/10.3390/microorganisms11061464 - 31 May 2023

Viewed by 182

Abstract

Considering the ban on the use of antibiotics as growth stimulators in the livestock industry, the use of microbiota modulators appears to be an alternative solution to improve animal performance. This review aims to describe the effect of different families of modulators on the gastrointestinal microbiota of poultry, pigs and ruminants and their consequences on host physiology. To this end, 65, 32 and 4 controlled trials or systematic reviews were selected from PubMed for poultry, pigs and ruminants, respectively. Microorganisms and their derivatives were the most studied modulator family in poultry, while in pigs, the micronutrient family was the most investigated. With only four controlled trials selected for ruminants, it was difficult to conclude on the modulators of interest for this species. For some modulators, most studies showed a beneficial effect on both the phenotype and the microbiota. This was the case for probiotics and plants in poultry and minerals and probiotics in pigs. These modulators seem to be a good way for improving animal performance. Full article

(This article belongs to the Special Issue Gut Microbiome of Farm Animals in Health and Disease 2.0)

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